Abstract
In recent years, next-generation sequencing technologies have been widely used, and are rapidly changing the landscape of genetics with unimaginable speed. However, the preliminary quality control regulations including trimming adaptor sequences, quality statistics, and depth and coverage statistics need to be applied to raw reads before further analysis. QACtools implements various utilities for processing raw reads in the FASTQ format and alignments in the BAM format. It analyzes some relevant properties of next-generation sequencing data such as average read length, base quality scores, and so on. Additionally, to our knowledge, none of the other tools support depth and coverage statistic that have been provided in our tool for analysis of large DNA sequencing data. It is crucial for overcoming errors in base calling and assembly. We suppose tool is useful for the quality control of NGS data to perform further analysis. This software is an open source application freely available at https://sourceforge.net/projects/qactools/.
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References
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135–1145
Siepel A, Pollard KS, Haussler D (2006). New methods for detecting lineage-specific selection. In: Adam S, Katherine SP, David H (eds) Research in computational molecular biology, Springer, pp 190–205
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767–1771
Meyerson M, Gabriel S, Getz G (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11(10):685–696
Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24(3):133–141
Li H, Handsaker B, Wysoker F, Ruan J, Homer N et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079
Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT (2011) BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics 27(12):1691–1692
Ajay SS, Parker SC, Abaan HO, Fajardo KV, Margulies EH (2011) Accurate and comprehensive sequencing of personal genomes. Genome Res 21(9):1498–1505
Patel RK, Jain M (2012) NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS One 7(2):e30619
Hampton M, Melvin RG, Kendall AH, Kirkpatrick BR, Peterson N, Andrews MT (2011) Deep sequencing the transcriptome reveals seasonal adaptive mechanisms in a hibernating mammal. PLoS One 6(10)
FastQC A quality control tool for high throughput sequence data. Simon Andrews. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Acknowledgments
This work was funded by the National Program on Key Basic Research Project (973 Program, Grant No. 2013CB329605), National Key Technology R&D Program of China (2012BAK11B01), National Natural Science Foundation of China (NSFC, Grant Nos. 61472040 and 60873237), Bei**g Higher Education Young Elite Teacher Project (Grant No. YETP1198).
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Song, D., Li, N., Liao, L. (2015). QACtools: A Quality Assessment and Quality Control Tool for Next-Generation Sequencing Data. In: Deng, Z., Li, H. (eds) Proceedings of the 2015 Chinese Intelligent Automation Conference. Lecture Notes in Electrical Engineering, vol 338. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-46466-3_46
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DOI: https://doi.org/10.1007/978-3-662-46466-3_46
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